1.siMacro: A Fast and Easy Data Processing Tool for Cell-Based Genomewide siRNA Screens.
Nitin Kumar SINGH ; Bo Yeun SEO ; Mathukumalli VIDYASAGAR ; Michael A WHITE ; Hyun Seok KIM
Genomics & Informatics 2013;11(1):55-57
Growing numbers of studies employ cell line-based systematic short interfering RNA (siRNA) screens to study gene functions and to identify drug targets. As multiple sources of variations that are unique to siRNA screens exist, there is a growing demand for a computational tool that generates normalized values and standardized scores. However, only a few tools have been available so far with limited usability. Here, we present siMacro, a fast and easy-to-use Microsoft Office Excel-based tool with a graphic user interface, designed to process single-condition or two-condition synthetic screen datasets. siMacro normalizes position and batch effects, censors outlier samples, and calculates Z-scores and robust Z-scores, with a spreadsheet output of >120,000 samples in under 1 minute.
High-Throughput Screening Assays
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RNA Interference
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RNA, Small Interfering
2.Surgical Treatment for Long Term Urethral Obstruction after Tension-Free Vaginal Tape Procedure.
Dae Sung CHO ; Yong Yeun WON ; Kyoung Sik SEO ; Min Kyu CHOI ; Jong Bo CHOI ; Young Soo KIM
Journal of the Korean Continence Society 2004;8(1):45-47
Most of anti-incontinence surgeries bear the risk of postoperative complication such as voiding dysfunction due to urethral obstruction. Fortunately, Tension Free Vaginal Tape(TVT) procedure has much lower incidence of postoperative urethral obstruction than other surgical procedures for stress urinary incontinence. There are many reports about the surgical treatments for short-term urethral obstruction after TVT procedure. However, there are few reports on the effect of surgical releasing of the obstruction lasting for a long period. In our case, the patient had urethral obstruction for 32 months after TVT procedure and she was able to void well after surgical releasing of the tape. We suggest that releasing of the tape will be a treatment of choice for long-term urethral obstruction after TVT procedure.
Humans
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Incidence
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Postoperative Complications
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Suburethral Slings*
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Urethral Obstruction*
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Urinary Incontinence
3.Variable number tandem repeat analysis of Mycobacterium bovis isolates from Gyeonggi-do, Korea.
Bo Young JEON ; Sungmo JE ; Jinhee PARK ; Yeun KIM ; Eun Gae LEE ; Hyeyoung LEE ; Sangkyo SEO ; Sang Nae CHO
Journal of Veterinary Science 2008;9(2):145-153
Bovine tuberculosis (TB) is a major zoonosis that's caused by Mycobacterium bovis (M. bovis). Being able to detect M. bovis is important to control bovine TB. We applied a molecular technique, the variable number tandem repeat (VNTR) typing method, to identify and distinguish the M. bovis isolates from Gyeonggi-do, Korea. From 2003 to 2004, 59 M. bovis clinical strains were isolated from dairy cattle in Gyeonggi-do, Korea, and these cattle had tuberculosis-like lesions. Twenty-four published MIRUVNTR markers were applied to the M. bovis isolates and ten of them showed allelic diversity. The most discriminatory locus for the M. bovis isolates in Korea was QUB 3336 (h = 0.64). QUB 26 and MIRU 31 also showed high discriminative power (h = 0.35). The allelic diversity by the combination of all VNTR loci was 0.86. Six loci (MIRU 31, ETR-A and QUB-18, -26, -3232, -3336) displayed valuable allelic diversity. Twelve genotypes were identified from the 59 M. bovis isolates that originated from 20 cattle farms that were dispersed throughout the region of Gyenggi-do. Two genotypes [designation index (d.i.) = e, g] showed the highest prevalence (20% of the total farms). For the multiple outbreaks on three farms, two successive outbreaks were caused by the same genotype at two farms. Interestingly, the third outbreak at one farm was caused by both a new genotype and a previous genotype. In conclusion, this study suggests that MIRU-VNTR typing is useful to identify and distinguish the M. bovis isolates from Gyeonggi-do, Korea.
Animals
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Cattle
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DNA Primers/genetics
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*Genetic Variation
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Genotype
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Korea/epidemiology
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Minisatellite Repeats/*genetics
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Mycobacterium bovis/*genetics
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Prevalence
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Tuberculosis, Bovine/*epidemiology/*microbiology
4.The Association of Perceived Neighborhood Walkability and Environmental Pollution With Frailty Among Community-dwelling Older Adults in Korean Rural Areas: A Cross-sectional Study
Mi Ji KIM ; Sung Hyo SEO ; Ae Rim SEO ; Bo Kyoung KIM ; Gyeong Ye LEE ; Yeun Soon CHOI ; Jin Hwan KIM ; Jang Rak KIM ; Yune Sik KANG ; Baek Geun JEONG ; Ki Soo PARK
Journal of Preventive Medicine and Public Health 2019;52(6):405-415
OBJECTIVES:
The aim of this study was to evaluate the associations of frailty with perceived neighborhood walkability and environmental pollution among community-dwelling older adults in rural areas.
METHODS:
The participants were 808 community-dwelling men and women aged 65 years and older in 2 rural towns. Comprehensive information, including demographics, socioeconomic status, grip strength, polypharmacy, perceived neighborhood environment (specifically, walkability and environmental pollution), and frailty, was collected from participants using face-to-face interviews conducted between June and August 2018. Perceived neighborhood walkability was measured using 20 items that were selected and revised from the Neighborhood Environment Walkability Scale, the Neighborhood Walkability Checklist from the National Heart Foundation of Australia, and the Physical Activity Neighborhood Environment Survey. The Kaigo-Yobo Checklist was used to assess participants’ frailty.
RESULTS:
The overall prevalence of frailty in this community-dwelling population was 35.5%. Sex, age, cohabitation status, educational attainment, employment status, grip strength, and polypharmacy were significantly associated with frailty. In the logistic regression analysis, frailty was associated with low perceived neighborhood walkability (adjusted odds ratio [aOR], 0.881; 95% confidence interval [CI], 0.833 to 0.932; p<0.001) and severe perceived neighborhood environmental pollution (aOR, 1.052; 95% CI, 1.017 to 1.087; p=0.003) after adjusting for sex, age, cohabitation status, educational attainment, employment status, monthly income, grip strength, and polypharmacy.
CONCLUSIONS
More studies are warranted to establish causal relationships between walkability and environmental pollution and frailty.
5.The Relationship between Hyperhomocysteinemia and C677T MTHFR Gene Polymorphism in Patients with Ischemic Stroke.
Sang Beom KIM ; Gue Yong LEE ; Jung Ho SEO ; Hyun Jo KIM ; Ok Joon KIM ; Bo Woo JUNG ; Do Yeun OH ; Nam Keun KIM ; Sun Hee KIM ; Kyung Cheon CHUNG ; Byung Ok CHOI
Journal of the Korean Neurological Association 2002;20(4):346-352
BACKGROUND: Hyperhomocysteinemia is an independent risk factor for cerebrovascular disease. MTHFR 677TT genotype can induce hyperhomocysteinemia. However, the association between this 677TT genotype and ischemic stroke still remains controversial. This study was undertaken to determine whether MTHFR 677TT genotype was associated with certain subtype of ischemic stroke. METHODS: The case group consisted of 129 patients with ischemic stroke and the control group consisted of 157 healthy individuals. We checked their fasting plasma homocysteine levels and analyzed the C677T mutation in the MTHFR gene. The relative risk of MTHFR 677TT genotype was assessed by odds ratios using multivariate logistic regression. RESULTS: Homocysteine levels in plasma were significantly higher in ischemic stroke patients (10.386.44 mol/L) than in controls (8.002.40) (P<0.05). In small-artery disease (11.366.01), the same result was found (P<0.05). On the other hand, the prevalence of the homozygote mutation was not significantly higher in ischemic stroke patients (20.2%) than in controls (13.4%) (adjusted OR 1.39, 95% CI 0.65 to 2.96). The adjusted OR and 95% CI was 2.59 (1.08 to 6.25) for the TT genotype in patients with small-artery disease compared to controls. The 677TT genotype was increased in small-artery disease compared to large-artery disease (adjusted OR 7.60, 95% CI 1.66 to 34.77). CONCLUSIONS: Our findings suggest that the homozygous C677T mutation in the MTHFR gene is a risk predictor in the subtype of ischemic stroke, such as small-artery disease.
Fasting
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Genotype
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Hand
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Homocysteine
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Homozygote
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Humans
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Hyperhomocysteinemia*
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Logistic Models
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Odds Ratio
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Plasma
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Prevalence
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Risk Factors
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Stroke*
6.Leptin is Negatively Associated with Femoral Bone Mineral Density in Postmenopausal Women with Type 2 Diabetes Mellitus.
Jae Han JEON ; Yeun Kyung CHOI ; Hyun Ae SEO ; Jung Eun LEE ; Ji Yun JEONG ; Seong Su MOON ; Ju Young LEE ; Jung Guk KIM ; Bo Wan KIM ; In Kyu LEE
Korean Diabetes Journal 2009;33(5):421-431
BACKGROUND: Serum leptin level and bone mineral density (BMD) are widely assumed to be positively associated with body fat mass. Numerous attempts have been made to document the relationship between leptin and BMD, but the results are inconsistent, especially in diabetic patients. METHODS: A total of 60 Korean postmenopausal women with type 2 diabetes mellitus were included in the present study. The BMDs of lumbar spines (L1 to L4) and proximal femurs (trochanter, neck, and total) were measured by dual-energy X-ray absorptiometry (DXA), and biochemical markers including leptin, HbA1c, C-peptide and urine albumin-creatinine ratio (ACR) were measured for each patient. RESULTS: Negative associations between leptin and BMD of femoral neck, trochanter, and total femur in postmenopausal women with type 2 diabetes mellitus were documented in a model adjusted for age, body fat mass, and fasting insulin level (r = -0.308, P = 0.020 and r = - 0.303, P = 0.025 and r = - 0.290, P = 0.032 respectively). Multiple linear regression analysis was performed revealing negative associations between leptin and BMD of the femoral neck (beta = -0.369), trochanter (beta = -0.324), and total femur (beta = -0.317). CONCLUSION: The results of the present study suggest a negative relationship between leptin and femoral BMD. In addition, leptin may have a negative effect on BMD in postmenopausal women with type 2 diabetes mellitus.
Absorptiometry, Photon
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Adipose Tissue
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Biomarkers
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Bone Density
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C-Peptide
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Diabetes Mellitus, Type 2
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Fasting
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Female
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Femur
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Femur Neck
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Humans
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Insulin
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Leptin
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Linear Models
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Neck
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Spine
7.Korean Thyroid Association Guidelines on the Management of Differentiated Thyroid Cancers; Overview and Summary 2024
Young Joo PARK ; Eun Kyung LEE ; Young Shin SONG ; Bon Seok KOO ; Hyungju KWON ; Keunyoung KIM ; Mijin KIM ; Bo Hyun KIM ; Won Gu KIM ; Won Bae KIM ; Won Woong KIM ; Jung-Han KIM ; Hee Kyung KIM ; Hee Young NA ; Shin Je MOON ; Jung-Eun MOON ; Sohyun PARK ; Jun-Ook PARK ; Ji-In BANG ; Kyorim BACK ; Youngduk SEO ; Dong Yeob SHIN ; Su-Jin SHIN ; Hwa Young AHN ; So Won OH ; Seung Hoon WOO ; Ho-Ryun WON ; Chang Hwan RYU ; Jee Hee YOON ; Ka Hee YI ; Min Kyoung LEE ; Sang-Woo LEE ; Seung Eun LEE ; Sihoon LEE ; Young Ah LEE ; Joon-Hyop LEE ; Ji Ye LEE ; Jieun LEE ; Cho Rok LEE ; Dong-Jun LIM ; Jae-Yol LIM ; Yun Kyung JEON ; Kyong Yeun JUNG ; Ari CHONG ; Yun Jae CHUNG ; Chan Kwon JUNG ; Kwanhoon JO ; Yoon Young CHO ; A Ram HONG ; Chae Moon HONG ; Ho-Cheol KANG ; Sun Wook KIM ; Woong Youn CHUNG ; Do Joon PARK ; Dong Gyu NA ;
International Journal of Thyroidology 2024;17(1):1-20
Differentiated thyroid cancer demonstrates a wide range of clinical presentations, from very indolent cases to those with an aggressive prognosis. Therefore, diagnosing and treating each cancer appropriately based on its risk status is important. The Korean Thyroid Association (KTA) has provided and amended the clinical guidelines for thyroid cancer management since 2007. The main changes in this revised 2024 guideline include 1) individualization of surgical extent according to pathological tests and clinical findings, 2) application of active surveillance in low-risk papillary thyroid microcarcinoma, 3) indications for minimally invasive surgery, 4) adoption of World Health Organization pathological diagnostic criteria and definition of terminology in Korean, 5) update on literature evidence of recurrence risk for initial risk stratification, 6) addition of the role of molecular testing, 7) addition of definition of initial risk stratification and targeting thyroid stimulating hormone (TSH) concentrations according to ongoing risk stratification (ORS), 8) addition of treatment of perioperative hypoparathyroidism, 9) update on systemic chemotherapy, and 10) addition of treatment for pediatric patients with thyroid cancer.